The genetic basis of heterosis in maize has been investigated in a number of studies but results have not been conclusive. Here, we compare quantitative trait loci (QTL) mapping results for grain yield, grain moisture, and plant height from three populations derived from crosses of the heterotic pattern Iowa Stiff Stalk Synthetic x Lancaster Sure Crop, investigated with the Design III, and analyzed with advanced statistical methods specifically developed to examine the genetic basis of mid-parent heterosis (MPH). In two populations, QTL analyses were conducted with a joint fit of linear transformations Z (1) (trait mean across pairs of backcross progenies) and Z (2) (half the trait difference between pairs of backcross progenies) to estimate augmented additive and augmented dominance effects of each QTL, as well as their ratio. QTL results for the third population were obtained from the literature. For Z (2) of grain yield, congruency of QTL positions was high across populations, and a large proportion of the genetic variance (~70%) was accounted for by QTL. This was not the case for Z (1) or the other two traits. Further, almost all congruent grain yield QTL were located in the same or an adjacent bin encompassing the centromere. We conclude that different alleles have been fixed in each heterotic pool, which in combination with allele(s) from the opposite heterotic pool lead to high MPH for grain yield. Their positive interactions very likely form the base line for the superior performance of the heterotic pattern under study.